Today’s topics

• RStudio (Projects & Setting/preferences)

• Generate reports from code (Quarto Scientific Publishing system)

• Publishing reports

You should have the latest version of Quarto!!

Reproducibility

Streaming previous workshops

R for Lunch: a lunchtime learning series

• IDE and Import data (RStudio IDE, Import data, Code notebook)
• Wrangle data {dplyr}
• Visualizing with {ggplot2}
• Mapping and Spatial Analysis

See Also: Online Resources: (Rfun | CDVS resources)

Housekeeping

• Drew / Lauren / breakout rooms
• CDVS
  • Themes

    • Data Management (Plans, Reproducibility, Repositories)

    • Data Science

    • Data Visualization

    • GIS and Spatial Analysis

    • Data Sources

Housekeeping continued

• Website - https://library.duke.edu/data
• Workshops
  • https://library.duke.edu/data/workshops
• Consulting in the Lab
  • askData@duke.edu
  • my schedule: https://is.gd/littleconsult

Ideal: R as a practical reproducible workflow

• Code in RStudio

• Report types: A select list of Quarto output formats

  • these slides (Live | Code and PDF on GitHub)
  • the Introduction to R/Tidyverse/Quarto text.
  • Manuscript: a framework for writing and publishing scholarly articles (live example)

• Use Git and GitHub for version control, code sharing, and collaboration

Projects

• Use the projects feature of RStudio

New Project > Quarto Project

• Do use code notebooks

• Do use relative file paths and {here}

• Do use Restart R and Run All Chunks

• Do not rewrite code for different computers

• Do not use setwd()

• Do not use rm(list=ls())

Reproducibility settings for your IDE

Citation management

Use a bibliography manager such as Zotero

Then,

RStudio > Quarto Notebook > Insert > Citation

Example DOI: 10.18637/jss.v059.i10

Publish

• Full Instructions

• Steps (simplified)

  1. In CLI (terminal, powershell, bash, etc.): quarto publish (For select Quarto project types)

  2. Choose a destination (e.g. quarto.pub or netlify.com)

Manuscript demo

• Live Demonstrations
  • my take | documented at GitHub
  • Posit documentation | documented

Instructions simplified

1. In CLI (e.g. RStudio Terminal, PowerShell, Bash, etc.):
   quarto create > project > manuscript
   • Identify LFS path / location
2. Go to that location; double-click <new_proj_name>.Rproj file (if using R)
3. usethis::use_git()
4. in _quarto.yml: change jats: default to pdf: default

{renv}

Create reproducible environments for your R projects by storing the exact versions of the code interpreter and r packages within the version-control repo

• Get Started
  • renv::init()
  • renv::snapshot()
  • and renv::restore()

Binder (Containers)

The Binder project makes it easy to share live compute environments. This is documented very well at Quarto.

In essence:

• CLI terminal: quarto use binder